Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:2.7.7.6 (RNA polymerase)
 34,946 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Mutated variants of the predicted promoter of the countertranscript of the Chlamydia trachomatis plasmid were tested by in vitro transcription with chlamydial extract. A 3-bp deletion within the -10 region of the putative promoter caused the RNA polymerase to initiate transcription 3 bases downstream. Many single mutations in the -10 and -35 regions did not alter promoter function. However, some multiple mutations in both hexamers rendered the promoter inefficient or ineffective. Taken together, these results indicate that (i) the sequence requirement for chlamydial promoters differs from that for Escherichia coli and (ii) chlamydial RNA polymerase can tolerate considerably more variation at the -10 and -35 regions. These results are paradoxical considering the homology between C. trachomatis sigma 66 and E. coli sigma 70.
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PMID:The RNA polymerase of Chlamydia trachomatis has a flexible sequence requirement at the -10 and -35 boxes of its promoters. 820 57

A 3.3-kb BamHI fragment from the center of the orf virus (OV) NZ2 genome has been sequenced, revealing three major open reading frames (ORFs) with homology to vaccinia virus (VAC) genes. These ORFs have been designated F2L, F3R, and F4R and the proteins they encode were found to be homologous to VAC genes H4L (RNA polymerase-associated protein RAP94), H5R (35-kDa virion envelope antigen) and H6R (topoisomerase), respectively. The OV ORFs are arranged on the genome in an almost identical manner to their VAC counterparts revealing the common evolutionary origin of the two viruses despite the extreme difference in their G+C content. Like its VAC counterpart, F3R was shown to be transcribed early and late during infection. S1 and primer extension analysis located the 5' ends of F3R early transcripts to a position 15-16 nt and 5-10 nt, respectively, downstream from an AT-rich sequence resembling a VAC early promoter. The 5' ends of F3R late transcripts were located to an A within the sequence 5'-TAAAG, 41 nt downstream from the early promoter and 17 nt upstream from the initiation codon. S1 analysis of F2L, which is transcribed only late in infection, revealed transcripts initiating from within the sequence 5'-TAAATG. No transcriptional start point could be detected for F4R but the VAC late transcriptional initiation sequence TAAAT was found close to the predicted translational start point. Another late promoter-like sequence, 5'-TAAATG, was found at the 3' end of F2L. This preceded a short ORF tentatively designated as F1L and predicted to be the beginning of a homologue of VAC H3L.
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PMID:Conservation of gene structure and arrangement between vaccinia virus and orf virus. 831 94

A 3.6-kb BglII-SmaI segment of the transfer region of IncI1 plasmid R64drd-11 was sequenced and characterized. Analysis of the DNA sequence indicated the presence of four genes, traA, traB, traC, and traD, in this region. The expression of the traB, traC, and traD genes was examined by maxicell experiments and that of the traA gene was examined by constructing the traA-lacZ fusion gene. The introduction of frameshift mutations into the four genes indicated that the traB and traC genes are essential for conjugal transfer in liquid medium and on a solid surface. Both were also required for the formation of the thin pilus, which is the receptor for phages I alpha and PR64FS. Upstream of the traA gene, a promoter sequence for sigma 70 of E. coli RNA polymerase was identified by S1 nuclease mapping and primer extension experiments.
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PMID:Nucleotide sequence and characterization of the traABCD region of IncI1 plasmid R64. 834 45

The genome of Lelystad virus (LV), the causative agent of porcine epidemic abortion and respiratory syndrome (previously known as mystery swine disease), was shown to be a polyadenylated RNA molecule. The nucleotide sequence of the LV genome was determined from a set of overlapping cDNA clones. A consecutive sequence of 15,088 nucleotides was obtained. Eight open reading frames (ORFs) that might encode virus-specific proteins were identified. ORF1a and ORF1b are predicted to encode the viral RNA polymerase because the amino acid sequence contains sequence elements that are conserved in RNA polymerases of the torovirus Berne virus (BEV), equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV), the coronaviruses, and other positive-strand RNA viruses. A heptanucleotide slippery sequence (UUUAAAC) and a putative pseudoknot structure, which are both required for efficient ribosomal frameshifting during translation of the RNA polymerase ORF1b of BEV, EAV, and the coronaviruses, were identified in the overlapping region of ORF1a and ORF1b of LV. ORFs 2 to 6 probably encode viral membrane-associated proteins, whereas ORF7 is predicted to encode the nucleocapsid protein. Comparison of the amino acid sequences of the ORFs identified in the genome of LV, LDV, and EAV indicated that LV and LDV are more closely related than LV and EAV. A 3' nested set of six subgenomic RNAs was detected in LV-infected cells. These subgenomic RNAs contain a common leader sequence that is derived from the 5' end of the genomic RNA and that is joined to the 3' terminal body sequence. Our results indicate that LV is closely related evolutionarily to LDV and EAV, both members of a recently proposed family of positive-strand RNA viruses, the Arteriviridae.
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PMID:Lelystad virus, the causative agent of porcine epidemic abortion and respiratory syndrome (PEARS), is related to LDV and EAV. 851 32

A 3'-terminal mutation of the gene encoding the beta subunit of Escherichia coli RNA polymerase was isolated using an in vivo polA(Ts) technique. Cloning of the allele was monitored by virtue of the fact that the deletion delta(rpoB)1570-1 resulted in an altered-size restriction fragment. DNA sequencing confirmed the predicted nature and location of the mutation: delta(rpoB)1570-1 involved an in-frame deletion of 186 bp (62 codons) encoding amino acid residues 967-1028. The phenotype conferred by delta(rpoB)1570-1 is discussed with respect to conserved domains within the beta polypeptide.
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PMID:In vivo cloning of a carboxy-terminal rpoB allele which confers altered transcriptional properties. 876 49

Met-ase-1 is a 30 000 Mr serine protease (granzyme) that was first isolated in the cytolytic granules of rat CD3(-) large granular lymphocytes. We screened a mouse genomic library with rat Met-ase-1 cDNA, and obtained bacteriophage clones that contained the mouse Met-ase-1 gene. The mouse Met-ase-1 gene comprises five exons spanning approximately 5.2 kilobases (kb) and exhibits a similar structural organization to its rat homologue and a family of neutrophil elastase-like serine proteases. Mouse Met-ase-1 mRNA was only detected in total cellular and poly A mRNA of mouse CD3(-) GM1(+) large granular lymphocytes derived from splenocytes stimulated with IL-2 and the mouse NK1.1(+) cell line 4 - 16. Spleen T-cell populations generated by Concanavalin A stimulation and a number of mouse pre-NK and T cell lines did not express mouse Met-ase-1 mRNA. The 5' flanking region of the mouse Met-ase-1 gene also shares considerable regions of identity with the 5' flanking region of the rat Met-ase-1 gene. A 3.3 kb segment of 5' sequence flanking the mouse Met-ase-1 gene was inserted upstream of the chloramphenicol acetyltransferase reporter gene and this construct transiently transfected into a variety of mouse and rat large granular lymphocyte leukemia and T-cell lines. The transcriptional activity of the mouse Met-ase-1 5' flanking region was significant in the RNK-16 large granular lymphocyte leukemia, strongest in the 4 - 16 mouse NK1.1(+) cell line, and weak in several mouse pre-NK cell lines. Reverse transcriptase polymerase chain reaction of mouse large granular lymphocyte mRNA was used to derive the full-length coding sequence for mouse Met-ase-1. The predicted hexapropeptide of mouse Met-ase-1 (Asn-6 to Gln-1), was deleted by polymerase chain reaction mutagenesis to enable expression of active mouse Met-ase-1 in mammalian COS-7 cells. Northern blot analysis and protease assays of transfected COS cell lysates against a panel of thiobenzyl ester substrates formally demonstrated that the mouse Met-ase-1 gene encodes a serine proteinase that hydrolyzes substrates containing a long narrow hydrophobic amino acids like methionine, norleucine, and leucine in the P1.
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PMID:Cloning and expression of the recombinant mouse natural killer cell granzyme Met-ase-1. 878 Nov 19

The rpoA gene, encoding the alpha subunit of RNA polymerase, was isolated from alkaliphilic Bacillus sp. strain C-125 by the PCR method. A 3-kb HindIII fragment containing the complete rpoA gene was cloned and sequenced. The alpha subunit gene was found to encode a protein consisting of 314 amino acid residues with a molecular mass of 34,805 Da. Compared with the amino acid sequences of other known eubacterial RNA polymerase alpha subunits, the gene has 84% identity to that of B. subtilis, while showing 48% and 47% identity to that of Streptomyces coelicolor and Escherichia coli, respectively. Six conserved regions, which are observed in the case of other eubacteria, were found in the RNA polymerase alpha subunit of this strain. Five of them are located in the N-terminal domain involved in assembly of the core enzyme, while one is located in the C-terminal domain, which interacts with several transcriptional factors and a specific DNA element. By means of recombinant plasmids, a hexahistidine-tagged derivative of the RNA polymerase alpha subunit of strain C-125 and two deletion derivatives (C- and N-terminal domains) of this protein were overexpressed in E. coli cells and purified to near homogeneity.
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PMID:Cloning and expression of the gene encoding RNA polymerase alpha subunit from alkaliphilic Bacillus sp. strain C-125. 983 38

We identified a Norwalk-like calicivirus (CV) whose genome likely was derived from naturally occurring recombination. This strain (Arg320) was detected by the EIA developed against recombinant Mexico virus (rMxV) capsids, but the viral RNA polymerase sequence was closer to Lordsdale virus, in a separate genetic cluster of Norwalk-like viruses. A 3.3 kb cDNA from the RNA polymerase region to the 3' end of the genome of Arg320 was cloned and sequenced. The sequence demonstrated that the capsid region of Arg320 shared 95% amino acid identity with MxV, but 68% identity with Lordsdale virus, while the RNA polymerase region shared 95% identity with Lordsdale virus, but 87% identity with MxV. Pair-wise sequence comparisons identified a potential recombination site at the polymerase/capsid junction. This is the first example of a naturally occurring recombinant in the CV family. Further studies to search for and characterize other strains may be necessary for understanding the genetic diversity of the family.
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PMID:Characterization of a novel human calicivirus that may be a naturally occurring recombinant. 1066 91

A 3'-truncated EBER2 RNA gene, although containing all previously identified promoter elements, revealed drastically reduced transcription rates in vitro and in vivo when fused to a heterologous terminator sequence. Inactivations were also observed with double point mutations affecting 5'- or 3'-end sequences of the EBER2 gene. However, wild-type activity of these mutants could be restored by compensatory mutations of the opposite strand of the EBER2 RNA sequence. A similar rescue was achieved with the 3'-truncated EBER2 gene, if the heterologous terminator was adapted for complementarity to the initiator element of the construct. Yet, double-strandedness alone of the RNA ends was not sufficient for high transcriptional activity of these gene constructs. Rather, the use of a nonrefoldable spacer, separating the 5'- and 3'-stem-loop structures, demonstrated that spatial proximity of the ends of EBER2 RNA was required. Furthermore, decay kinetics of wild-type and mutant RNA synthesized in vitro indicated that the effects observed could not be explained by altered transcript stability. Finally, single-round transcription confirmed that the reduced expression of mutant genes was not caused by decreased primary initiation reactions. In addition, differential sarcosyl concentrations demonstrated that the rate of reinitiation clearly was affected with the mutant EBER2 genes. Together, these results indicate that the secondary structure of this viral RNA represents a major determinant for efficient transcription of the EBER2 gene by host cell RNA polymerase III.
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PMID:Efficient transcription of the EBER2 gene depends on the structural integrity of the RNA. 1264 95

Actinomycin-D is an antineoplastic agent that inhibits RNA synthesis by binding to guanine residues and inhibiting DNA-dependent RNA polymerase. Although actinomycin-D has been used to treat rhabdomyosarcoma and Wilms tumor for more than 40 years, the dose/exposure relationship is not well characterized. The objective of this study was to develop an initial population pharmacokinetic model to describe actinomycin-D disposition in children and young adults from which a prospective study could be designed. A total of 165 actinomycin-D plasma concentration measurements from 33 patients, aged 1.6 to 20.3 years, were used for the analysis. The data were analyzed using nonlinear mixed-effects modeling with the NONMEM software system. Age, weight, and gender were examined as covariates for the ability to explain interindividual variability in actinomycin-D pharmacokinetics. The final model was qualified via predictive check and nonparametric bootstrap procedures. A 3-compartment model with first-order elimination was chosen as the structural model. Allometric expressions incorporating weight were used to describe the effects of body size on actinomycin-D pharmacokinetics. Age and gender had no discernible effects on actinomycin-D pharmacokinetics in the population studied. The predictive check showed that the developed model was able to simulate data in close agreement with the actual study observations. The availability of an initial population pharmacokinetic model to describe actinomycin-D pharmacokinetics will facilitate the development of a large-scale clinical trial to study the actinomycin-D dose/exposure relationship in pediatric patients with rhabdomyosarcoma and Wilms tumor. The covariate analysis described by the current data set suggests that indices of body size captured via allometric expressions improve the partition of variation in actinomycin-D pharmacokinetics from this pilot data set. Relationships between pharmacokinetics and toxicity will be examined in future prospective studies in which children less than 1 year old will be enrolled.
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PMID:Population pharmacokinetic investigation of actinomycin-D in children and young adults. 1809 18


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